MCC's law 19.8, which deals with overthrows, says: "If the boundary results from an overthrow... runs scored shall be any runs for penalties awarded... and allowance for the boundary, and runs completed by batsmen, together with the run in progress if they had already crossed at the instant of the throw or act."
The governing International Cricket Council could not be immediately reached for comment about the decision of the umpires.
Cricket website ESPNcricinfo reported after reviewing footage that Guptill had released the ball when Stokes and Adil Rashid had not yet crossed for the second run.
Taufel said leg-spinner Rashid would have been on strike to face the last two deliveries had the second run been found to be incomplete.
However, he had sympathy for Sri Lankan umpire Kumar Dharmasena and his South African colleague Marais Erasmus, the men in the middle.